The effects of plant growth promoting rhizobacteria (PGPR) on the rooting and root growth of semi-hardwood and hardwood kiwifruit stem cuttings were investigated. The PGPR used were Bacillus RC23, Paenibacillus polymyxa RC05, Bacillus subtilis OSU142, Bacillus RC03, Comamonas acidovorans RC41, Bacillus megaterium RC01 and Bacillus simplex RC19. All the bacteria showed indole-3-acetic acid (IAA) producing capacity. Among the PGPR used, the highest rooting ratios were obtained at 47.50% for semi-hardwood stem cuttings from Bacillus RC03 and Bacillus simplex RC19 treatments and 42.50% for hardwood stem cuttings from Bacillus RC03. As well, Comamonas acidovorans RC41 inoculations indicated higher value than control treatments. The results suggest that these PGPR can be used in organic nursery material production and point to the feasibility of synthetic auxin (IBA) replacement by organic management based on PGPR.

采用Illumina Miseq高通量测序平台，对木霉LTR-2拌种剂拌种小麦后不同发育时期小麦根际土壤真菌进行测序，分析群落丰富度、多样性以及结构。结果表明，木霉拌种处理小麦可以增加小麦根际真菌群落的丰富度，对真菌群落的均匀度影响不明显，但真菌群落的优势度有明显的增加；木霉拌种处理后小麦根际土壤真菌的菌群结构构成相近，没有发生明显变化，但各真菌类群所占比例发生了明显的变化，其中一些病原真菌如链格孢属、赤霉属、镰刀菌属所占比例较不拌种处理均有所降低。该研究为木霉菌LTR-2防治小麦土传病害的生防机制提供了理论依据。

Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over earlier methods. In this Review, we discuss the best practices for performing a microbiome study, including experimental design, choice of molecular analysis technology, methods for data analysis and the integration of multiple omics data sets. We focus on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis, where advances have been particularly rapid. We note that although some of these approaches are new, it is important to keep sight of the classic issues that arise during experimental design and relate to research reproducibility. We describe how keeping these issues in mind allows researchers to obtain more insight from their microbiome data sets.

The production of 'global' metabolite profiles involves measuring low molecular-weight metabolites (<1 kDa) in complex biofluids/tissues to study perturbations in response to physiological challenges, toxic insults or disease processes. Information-rich analytical platforms, such as mass spectrometry (MS), are needed. Here we describe the application of ultra-performance liquid chromatography-MS (UPLC-MS) to urinary metabolite profiling, including sample preparation, stability/storage and the selection of chromatographic conditions that balance metabolome coverage, chromatographic resolution and throughput. We discuss quality control and metabolite identification, as well as provide details of multivariate data analysis approaches for analyzing such MS data. Using this protocol, the analysis of a sample set in 96-well plate format, would take ca. 30 h, including 1 h for system setup, 1-2 h for sample preparation, 24 h for UPLC-MS analysis and 1-2 h for initial data processing. The use of UPLC-MS for metabolic profiling in this way is not faster than the conventional HPLC-based methods but, because of improved chromatographic performance, provides superior metabolome coverage.

White tea is considered the least processed form of tea and is reported to have a series of potent bioactivities, such as antioxidant, anti-inflammatory, anti-mutagenic, and anti-cancer activities. However, the chemical composition of white tea and the dynamic changes of the metabolites during the manufacturing process are far from clear. In this study, we applied a nontargeted metabolomics approach based on ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF/MS) to comprehensively profile the characteristic metabolites of white tea. There were significant differences in the content of amino acids, catechins, dimeric catechins, flavonol and flavone glycosides, and aroma precursors in white tea compared with green and black teas that were manufactured from the same fresh tea leaves. Furthermore, the dynamic changes of the metabolites in the tea samples with various withering durations of 0, 4, 8, 12, 16, 20, 24, 28, and 36 h were also profiled. This study offers a comprehensive characterization of the metabolites and their changes in white tea.Copyright © 2017. Published by Elsevier Ltd.

目的 探讨根际促生菌（plant-growth promoting rhizobacteria, PGPR）共发酵菌液制备的生物育苗基质对穴盘育苗条件下辣椒幼苗生长的影响及作用机制，为生物育苗基质的研发奠定基础。 方法 通过4株PGPR菌株的兼容性分析、不同菌株组合共发酵液的吲哚乙酸（indoleacetic acid, IAA）含量测定及对辣椒的浸种实验以筛选共发酵菌株；通过穴盘育苗分析共发酵菌液对辣椒种子萌发及幼苗长势的影响以确定生物育苗的菌株组合；通过不同比例共发酵液添加对苗盘期幼苗的生长影响以确定其最适添加量；通过分析共发酵菌液对育苗基质营养物质含量及微生物多样性的影响以解析其促进幼苗生长的机制。 结果 吡咯伯克霍尔德氏菌P10和弯曲芽胞杆菌HGD12菌株的共发酵液含有60.84 mg/L IAA，显著高于2个菌株的单菌培养液，且明显促进了浸种和穴盘育苗条件下辣椒种子的萌发和幼苗的长势。15%共发酵液添加到育苗基质中，对苗盘期幼苗的促生长作用最优，辣椒幼苗的株高、茎粗、鲜重、干重、叶片数、叶面积及叶绿素SPAD值分别显著提高29.17%、17.67%、64.68%、94.44%、22.30%、49.45%及17.83%，基质的有机质、碱解氮及可溶磷含量分别增加了11.31%、20.39%及14.14%。而且，共发酵菌液显著提高了基质的细菌物种丰度并降低了真菌的群落多样性，与基质营养物质含量显著正相关的拟杆菌门、芽单胞菌门、绿弯菌门、嗜盐菌门、罗兹菌门及担子菌门的丰度提高，而与其负相关的变形菌门、子囊菌门、球囊菌门等的丰度降低。 结论 P10和HGD12菌株的共发酵液添加到育苗基质中，可以提高基质的营养物质含量及改变基质的微生物群落结构，显著促进辣椒种子的萌发及苗盘期幼苗的生长。

\n Abstract.\n Temporal variations in the spatial distribution of fine‐root mass and nutrient concentrations were studied in recently harvested and mature bamboo savanna sites in the dry tropical Vindhyan region in India. The soil block method and root‐free‐soil cages were used to investigate fine‐root dynamics. The mean annual fine‐root biomass was 596 and 690 g/m\n 2\n in harvested and mature sites, respectively. The fine‐root net production calculated by different methods ranged from 486 to 749 g m\n ‐2\n yr\n ‐1\n in the harvested site and 485 to 875 g m\n ‐2\n yr\n 1\n in the mature site. All fine‐root mass fractions decreased with increase in distance from the base of bamboo clumps, and the herb root mass showed the reverse trend. Bamboo fine roots were better developed in the 10 ‐ 20 cm soil depth and those of herbs in the upper 10 cm. The ingrowth of fine roots in root‐free‐soil cages showed maximum biomass accumulation during the rainy season (64.2 ‐ 69.9 g m\n ‐2\n mo\n ‐1\n ) and minimum in the summer (4.5 ‐ 7.5 g m\n ‐2\n mo\n ‐1\n ). The fine‐root nutrient concentrations were strongly related to their diameter. The fine‐root nutrient concentrations varied considerably in different seasons. The highest nutrient concentrations in all categories were recorded in summer followed by winter and rainy seasons. Nutrient concentrations in live roots were always greater than those found in dead roots in different diameter classes. We suggest the occurrence of nutrient retranslocation from senescent roots to surviving roots in bamboo savanna. Fine roots in the bamboo savanna increased as a function of N‐mineralization and nitrification rates. This tendency further increased after the harvest of bamboo, suggesting the crucial role of fine roots in the bamboo savanna after the harvesting of bamboo culms.\n

为探究生物菌剂木霉菌对切花月季病害的防控效果，在月季苗期施用300倍木霉菌可湿性粉剂。结果表明，施用木霉菌可促进和丰富月季根际、根内的真菌物种种类分布，对土壤中真菌及根内微生物多样性影响较大，OTU个数增加，特别根际真菌指数Shannon、Simpson及PD指数均高于清水对照和化学药剂甲基硫菌灵，说明施用木霉菌后使土壤真菌种类更加丰富，而且提高了一些有益菌的丰度。从对月季霜霉病的防治效果来看，300倍木霉菌及800倍50%甲基硫菌灵3次施药后相比清水对照均表现出显著差异，木霉菌防病和治疗效果达87.35%，比化学药剂甲基硫菌灵防效略高。

Agricultural productivity relies on a wide range of ecosystem services provided by the soil biota. Plowing is a fundamental component of conventional farming, but long-term detrimental effects such as soil erosion and loss of soil organic matter have been recognized. Moving towards more sustainable management practices such as reduced tillage or crop residue retention can reduce these detrimental effects, but will also influence structure and function of the soil microbiota with direct consequences for the associated ecosystem services. Although there is increasing evidence that different tillage regimes alter the soil microbiome, we have a limited understanding of the temporal dynamics of these effects. Here, we used high-throughput sequencing of bacterial and fungal ribosomal markers to explore changes in soil microbial community structure under two contrasting tillage regimes (conventional and reduced tillage) either with or without crop residue retention. Soil samples were collected over the growing season of two crops (Vicia faba and Triticum aestivum) below the seedbed (15-20 cm). Tillage, crop and growing stage were significant determinants of microbial community structure, but the impact of tillage showed only moderate temporal dependency. Whereas the tillage effect on soil bacteria showed some temporal dependency and became less strong at later growing stages, the tillage effect on soil fungi was more consistent over time. Crop residue retention had only a minor influence on the community. Six years after the conversion from conventional to reduced tillage, soil moisture contents and nutrient levels were significantly lower under reduced than under conventional tillage. These changes in edaphic properties were related to specific shifts in microbial community structure. Notably, bacterial groups featuring copiotrophic lifestyles or potentially carrying the ability to degrade more recalcitrant compounds were favored under conventional tillage, whereas taxa featuring more oligotrophic lifestyles were more abundant under reduced tillage. Our study found that, under the specific edaphic and climatic context of central Belgium, different tillage regimes created different ecological niches that select for different microbial lifestyles with potential consequences for the ecosystem services provided to the plants and their environment.

Managing ecosystems to maintain biodiversity may be one approach to ensuring their dynamic stability, productivity, and delivery of vital services. The applicability of this approach to industrial ecosystems that harness the metabolic activities of microbes has been proposed but has never been tested at relevant scales. We used a tag-sequencing approach with bacterial small subunit rRNA (16S) genes and eukaryotic internal transcribed spacer 2 (ITS2) to measuring the taxonomic composition and diversity of bacteria and eukaryotes in an open pond managed for bioenergy production by microalgae over a year. Periods of high eukaryotic diversity were associated with high and more-stable biomass productivity. In addition, bacterial diversity and eukaryotic diversity were inversely correlated over time, possibly due to their opposite responses to temperature. The results indicate that maintaining diverse communities may be essential to engineering stable and productive bioenergy ecosystems using microorganisms.

Despite the importance of microbial communities for ecosystem services and human welfare, the relationship between microbial diversity and multiple ecosystem functions and services (that is, multifunctionality) at the global scale has yet to be evaluated. Here we use two independent, large-scale databases with contrasting geographic coverage (from 78 global drylands and from 179 locations across Scotland, respectively), and report that soil microbial diversity positively relates to multifunctionality in terrestrial ecosystems. The direct positive effects of microbial diversity were maintained even when accounting simultaneously for multiple multifunctionality drivers (climate, soil abiotic factors and spatial predictors). Our findings provide empirical evidence that any loss in microbial diversity will likely reduce multifunctionality, negatively impacting the provision of services such as climate regulation, soil fertility and food and fibre production by terrestrial ecosystems.

There has recently been a surge of literature examining microbial invasions into a variety of environments. These studies often include a component of biological diversity as a major factor determining an invader's fate, yet common results are rarely cross-compared. Since many studies only present a snapshot of the entire invasion process, a bird's eye view is required to piece together the entire continuum, which we find consists of introduction, establishment, spread, and impact phases. We further examine the patterns and mechanisms associated with invasion resistance and create a mechanistic synthesis governed by the species richness, species evenness, and resource availability of resident communities. We conclude by exploring the advantages of using a theoretical invasion framework across different fields. Copyright © 2015 Elsevier Ltd. All rights reserved.

The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance. Pseudomonadaceae, bacillaceae, solibacteraceae and cytophagaceae were more abundant in the rhizosphere of the Fox-resistant cultivar. Network analyses showed a modular topology of the rhizosphere microbiome of the Fox-resistant cultivar, suggesting a more complex and highly connected bacterial community than in the rhizosphere of the Fox-susceptible cultivar. Metagenome analyses further revealed that specific functional traits such as protein secretion systems and biosynthesis genes of antifungal phenazines and rhamnolipids were more abundant in the rhizobacterial community of the Fox-resistant cultivar. Our findings suggest that breeding for Fox resistance in common bean may have co-selected for other unknown plant traits that support a higher abundance of specific beneficial bacterial families in the rhizosphere with functional traits that reinforce the first line of defense.

This study was conducted to assess the effect of thermophilic actinomycetes inoculation on the lignocellulose degradation, enzyme activities and microbial community during different types of straw composting from wheat, rice, corn and soybean. The results showed that actinomycetes inoculation not only changed the structure of actinomycetic and bacterial community but also accelerated the degradation of cellulose, hemicellulose and lignin and increased the key enzymes activities including CMCase, Xylanase, manganese peroxidase, lignin peroxidase and laccase during composting particularly from wheat straw and rice straw. The key enzyme and physiochemical parameters which affected organic fractions degradation have been identified by redundancy analysis. The combined application of actinomycete inoculation and urea addition as a source of nitrogen was suggested to regulate the key enzyme activities and lignocellulose degradation, which lays a foundation for effectively managing organic wastes from different types of crop straws by composting.Copyright © 2018 Elsevier Ltd. All rights reserved.